Mercurial > repos > galaxyp > openms_proteinquantifier
diff ProteinQuantifier.xml @ 13:d426affe977c draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:18:55 +0000 |
| parents | bb1e75938909 |
| children |
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--- a/ProteinQuantifier.xml Fri Nov 06 20:23:27 2020 +0000 +++ b/ProteinQuantifier.xml Thu Dec 01 19:18:55 2022 +0000 @@ -1,13 +1,11 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Quantitation]--> -<tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Compute peptide and protein abundances</description> <macros> <token name="@EXECUTABLE@">ProteinQuantifier</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -86,44 +84,44 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> - <param name="protein_groups" argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/> - <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> - <param name="top" argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/> - <param name="average" argument="-average" display="radio" type="select" optional="false" label="Averaging method used to compute protein abundances from peptide abundances" help=""> + <param argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> + <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/> + <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> + <param argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/> + <param argument="-average" type="select" optional="true" label="Averaging method used to compute protein abundances from peptide abundances" help=""> <option value="median" selected="true">median</option> <option value="mean">mean</option> <option value="weighted_mean">weighted_mean</option> <option value="sum">sum</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="average"/> </param> - <param name="include_all" argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/> - <param name="best_charge_and_fraction" argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/> - <param name="greedy_group_resolution" argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/> - <param name="ratios" argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) "/> - <param name="ratiosSILAC" argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)"/> + <param argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/> + <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/> + <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/> + <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) "/> + <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)"/> <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false"> <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/> - <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0', all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> + <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0',all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> </section> <section name="format" title="Output formatting options" help="" expanded="false"> <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="separator"/> </param> - <param name="quoting" argument="-format:quoting" display="radio" type="select" optional="false" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> + <param name="quoting" argument="-format:quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> <option value="none">none</option> <option value="double" selected="true">double</option> <option value="escape">escape</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="quoting"/> </param> <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="replacement"/> </param> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -150,13 +148,387 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_ProteinQuantifier"/> - <expand macro="manutest_ProteinQuantifier"/> + <tests><!-- TOPP_ProteinQuantifier_1 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.featureXML"/> + <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="median"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_2 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.featureXML"/> + <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="2"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="true"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_3 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_3_input.featureXML"/> + <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="2"/> + <param name="average" value="mean"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="0"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_7 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="0"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_8 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_9 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_12 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="true"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_13 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.consensusXML"/> + <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="3"/> + <param name="average" value="sum"/> + <param name="include_all" value="true"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="true"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="true"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_ProteinQuantifier_14 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="ProteinQuantifier_input.idXML"/> + <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="top" value="0"/> + <param name="average" value="sum"/> + <param name="include_all" value="false"/> + <param name="best_charge_and_fraction" value="false"/> + <param name="greedy_group_resolution" value="false"/> + <param name="ratios" value="false"/> + <param name="ratiosSILAC" value="false"/> + <section name="consensus"> + <param name="normalize" value="false"/> + <param name="fix_peptides" value="false"/> + </section> + <section name="format"> + <param name="separator" value=""/> + <param name="quoting" value="double"/> + <param name="replacement" value="_"/> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Compute peptide and protein abundances -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ProteinQuantifier.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinQuantifier.html]]></help> <expand macro="references"/> </tool>